JoGo: Joint Open Genome and Omics Platform

Haplotype Detail Info [ACTRT1_chrX_128045962_128057403>a0001c0001t0001g0000]

geneid	139741
ensemblid	ENSG00000123165.9
hgncid	24027
symbol	ACTRT1
name	actin related protein T1
refseq_nuc	NM_138289.4
refseq_prot	NP_612146.1
ensembl_nuc	ENST00000371124.5
ensembl_prot	ENSP00000360165.3
mane_status	MANE Select
chr	chrX
start	128050962
end	128052403
strand	-
ver	v1.2
region	chrX:128050962-128052403
region5000	chrX:128045962-128057403
regionname0	ACTRT1_chrX_128050962_128052403
regionname5000	ACTRT1_chrX_128045962_128057403

chr:pos	ref	alt	af	annotation	impact	samples	AHAPIDS	ACHAPIDS	ACTHAPIDS	ACTGHAPIDS	ac	an	len	genename	geneid	featuretype	featureid	transcript_biotype	rank	hgvs_c	hgvs_p	cdna_pos_length	cds_pos_length	aa_pos_length	distance	status
chrX:128050964	G G	T T	0.0035	splice_region_variant splice_region_variant	LOW	NA18946.hp2 NA18946.hp2	a0001 a0001	a0001c0001 a0001c0001	a0001c0001t0005 a0001c0001t0005	a0001c0001t0005g0000 a0001c0001t0005g0000	1	285	0	ACTRT1	ENSG00000123165.9	transcript	ENST00000371124.5	protein_coding	1/1	c.*112C>A

chr:pos	ref	alt	af	annotation	impact	samples	ahapids	achapids	acthapids	actghapids	ac	an	len	genename	geneid	featuretype	featureid	transcript_biotype	rank	hgvs_c	hgvs_p	cdna_pos_length	cds_pos_length	aa_pos_length	distance	status

chr:pos	ref	alt	af	annotation	impact	samples	ahapids	achapids	acthapids	actghapids	ac	an	len	genename	geneid	featuretype	featureid	transcript_biotype	rank	hgvs_c	hgvs_p	cdna_pos_length	cds_pos_length	aa_pos_length	distance	status

chr:pos	ref	alt	annotation	impact	samples	ahapids	achapids	acthapids	actghapids	ac	an	af	len	genename	geneid	featuretype	featureid	transcript_biotype	rank	hgvs_c	hgvs_p	cdna_pos_length	cds_pos_length	aa_pos_length	distance	status

genename	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	ahapid	alen	total	AFR	AMR	EAS	EUR	SAS	aseq	chr	start	end
ACTRT1	1/1	a0001	376	269	66	52	117	8	24	subcellular location copy fasta	chrX	128045962	128057403

genename	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	chapid	clen	total	AFR	AMR	EAS	EUR	SAS	cseq	chr	start	end
ACTRT1	1/1	c0001	1131	269	66	52	117	8	24	copy fasta	chrX	128045962	128057403

genename	grch38/ chm13v2	thapid	tlen	total	AFR	AMR	EAS	EUR	SAS	tseq	chr	start	end
ACTRT1	1/1	t0001	312	258	58	50	118	6	24	copy fasta	chrX	128045962	128057403

genename	grch38/ chm13v2	ghapid	total	AFR	AMR	EAS	EUR	SAS	chr	start	end
ACTRT1	1/1	g0000	285	72	57	121	8	25	chrX	128045962	128057403

genename	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	achapid	total	AFR	AMR	EAS	EUR	SAS	clen	cseq	chr	start	end
ACTRT1	1/1	a0001c0001	269	66	52	117	8	24	1131	copy fasta	chrX	128045962	128057403

genename	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	acthapid	total	AFR	AMR	EAS	EUR	SAS	tlen	tseq	chr	start	end
ACTRT1	1/1	a0001c0001t0001	243	53	45	114	6	23	1442	copy fasta	chrX	128045962	128057403

genename	grch38/ chm13v2 1/0: The haplotype type is the same as GRCh38 0/1: The haplotype type is the same as CHM13v2 0/0: The haplotype type matches neither GRCh38 nor CHM13v2 1/1: The haplotype type is the same on both GRCh38 and CHM13v2	actghapid	total	AFR	AMR	EAS	EUR	SAS	chr	start	end
ACTRT1	1/1	a0001c0001t0001g0000	243	53	45	114	6	23	chrX	128045962	128057403

pos	S. Strand	E# Exon Number	max	median	min	diff	type	haplotypeid	max_hap_list	min_hap_list	symbol	chr	start	end

pos	annotation hgvs_c hgvs_p	clinvarid	clnsig	geneinfo	mc	clndisdb	strand strand	ahapid ahapid_count	chapid chapid count	thapid thapid_count	ghapid ghapid_count	AHAPIDS ahapids	ACHAPIDS achapids	ACTHAPIDS acthapids	ACTGHAPIDS actghapids	haplotypeids haplotypeids	impact	chr	ref	alt	external

CHR:POS	annotation hgvs_c hgvs_p	disease trait -log10p odds or beta	AHAPIDS ahapids	ACHAPIDS achapids	ACTHAPIDS acthapids	ACTGHAPIDS actghapids	haplotypeids haplotypeids	study	initial sample size/ replication sample size	report genes	mapped gene	strongest snp risk allele	strand strand	impact	chr	ref	alt

pos	genename hgvs_c hgvs_p annotation	tissue expression gene -log10(pval) slope Tissue name in GTEx database(the target eQTL tissue name of the GTEx database) The -log10(nominal pvalue) in GTEx database Slope in GTEx database (positive value:alt allele has higher gene expression)	ahapid chapid thapid ghapid ahapid_count chapid_count thapid_count ghapid_count	AHAPIDS ahapids	ACHAPIDS achapids	ACTHAPIDS acthapids	ACTGHAPIDS actghapids	haplotypeids haplotypeids	af allele frequency in GTEx database	ms The number of samples with minor allele in GTEx database	ma The number of minor allele count in GTEx database	ver GTEx version	vid Variant ID in GTEx database	strand strand	impact	chr	ref	alt	external